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compositions (version 1.40-3)

Compositional Data Analysis

Description

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

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Version

Install

install.packages('compositions')

Monthly Downloads

10,267

Version

1.40-3

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

October 25th, 2019

Functions in compositions (1.40-3)

Composition of glaciar sediments from the Aar massif (Switzerland)

Activity patterns of a statistician for 20 days

Color-size compositions of 20 clam colonies from East Bay

Permeabilities of bayesite

Activity patterns of a statistician for 20 days

AnimalVegetation

Animal and vegetation measurement

Compositions and depth of 25 specimens of boxite

Artic lake sediment samples of different water depth

Color-size compositions of 20 clam colonies from West Bay

Compositions, depths and porosities of 25 specimens of coxite

Household Expenditures

Steroid metabolite patterns in adults and children

Helper to compute confidence ellipsoids

Compositions of 25 specimens of kongite

CompLinModCoReg

Compositional Linear Model of Coregionalisation

White-cell composition of 30 blood samples by two different methods

Diagnostic probabilities

Proportions of supervisor's statements assigned to different categories

Count compositions

Hydrochemical composition data set of Llobregat river basin water (NE Spain)

Compositional Goodness of fit test

Firework mixtures

A biplot providing somewhat easier access to details of the plot.

Honk Kong Pogo-Jumps Championship

Compositions and total pebble counts of 92 glacial tills

Yatquat fruit evaluation

Measurement of skulls

Bar charts of amounts

Aitchison compositions

colorsForOutliers

Create a color/char palette or for groups of outliers

compositions-package

Treating binary and g-adic numbers

Correlations of amounts and compositions

Heuristics to find subpopulations of outliers

Dendrogram representation of acomp or rcomp objects

AFM compositions of 23 aphyric Skye lavas

Compositions of 25 specimens of hongite

gsigetBalStruct

An auxiliary functions to compute user-defined ilr and ipt transforms.

Internal function: row and column sums of matrices

Internal functions of the compositions package

Interal function: Get number of samples and number of parts in a compositional object

Proportions of sand, silt and clay in sediments specimens

Serum Protein compositions of blood samples

Internal functions of the compositions package

Compositional Ordinary Kriging

Internal function: Convert to plain vector or matrix

missing.compositions

The policy of treatment of missing values in the "compositions" package

Marginal compositions in Aitchison Compositions

Compute balances for a compositional dataset.

Power transform in the simplex

Drawing a 3D coordiante system to a plot, based on package rgl

Fitting a Dirichlet distribution

Isometric identity transform

Isometric log ratio transform

Hotellings T square distribution

Shifts of machine operators

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Internal function: give a derived subclass to an object

The geometric mean

Classical Gauss Test

Internal functions: Parallel operations of single and multiple datasets

Isometric planar transform

Check for compositional data type

The arithmetic mean of rows or columns

Mean amounts and mean compositions

SimulatedAmounts

Simulated amount datasets

Additive log ratio transform

vectorial arithmetic for data sets with aplus class

Internal functions: A conditional drop

Perturbation of compositions

Group amounts of parts

Amounts analysed in log-scale

powerofpsdmatrix

power transform of a matrix

Ternary diagrams

Three-dimensional biplots, based on package rgl

The canonical basis in the clr plane used for ilr and ipt transforms.

arrows in 3D, based on package rgl

Additive planar transform

Convert "compositions" classes to data frames

Centered log ratio transform

Displaying compositions and amounts with box-plots

Convert between clr and ilr, and between cpt and ipt.

Principal component analysis for amounts in log geometry

Principal component analysis for Aitchison compositions

Environment containing the old gsi functions

Internal functions of the compositions package

Internal functions of the compositions package

Internal functions of the compositions package

Internal function: Recode missings with IEEE number and vice versa

Principal component analysis for real compositions

Treating single compositions as one-row datasets

plot in 3D based on rgl

outlierclassifier

Detect and classify compositional outliers.

Internal function: Invert a permutation

Normal quantile plots for compositions and amounts

vectorial arithmetic for datasets in a classical vector scale

3D-plot of compositional data

Dirichlet distribution

inner product for datasets with vector scale

Centered default transform

Internal function: Checking equality of IEEE special numbers

Centered planar transform

Distances in variouse approaches

gsi.isSingleRow

Internal function: Can something be considered as a single multivariate data item?

Closure of a composition

Internal functions: Storing integers as reals

gsi.varwithlosts

Internal function: computes variance of compositional data set with missing/zero values

Isometric default transform

endmemberCoordinates

Recast amounts as mixtures of end-members

getdetectionlimit

Gets the detection limit stored in the data set

Simulate count compositions without overdispersion

The uniform distribution on the simplex

Compositional Goodness of fit test

gsi.expandrcomp

Internal function: Scaling rcomp

Isometric log transform

Calling from a function with the own parameters

The canonical basis in the clr plane used for ilr and ipt transforms.

Marginal compositions in real geometry

Draws straight lines from point to point.

Read standard data files

Reads a data file in a geoeas format

simplemissingplot

Ternary diagrams

Internal function: Compute a desired compositional margin

Internal function: Reshape an object to the shape type of another

gsi.merge2signary

Auxiliary functions to compute user-defined ilr and ipt transforms.

Internal functions of the compositions package

IsMahalanobisOutlier

Checking for outliers

isoPortionLines

Isoportion- and Isoproportion-lines

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Draws connected lines from point to point.

Reads a data file in a mixR format

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Internal function: Solves singular and non square equation systems

Internal functions of the compositions package

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

plotmissingsummary

Plot a Missing Summary

Internal function: A panel displaying a label only

Internal functions of the compositions package

Displaying amounts in scatterplots

logratioVariogram

Empirical variograms for compositions

missingProjector

Returns a projector the the observed space in case of missings.

Vector space norm

Principal component analysis for real data

3D-plot of positive data

plot in 3D based on rgl

Principal component analysis for real amounts

Normalize vectors to norm 1

Classify and summarize missing values in a dataset

Compositional Goodness of fit test

Summaries of amounts

Summary of compositions in real geometry

Variance covariance matrix of parameters in compositional regression

Aitchison Distribution

The names of the parts

plotlogratioVariogram

Empirical variograms for compositions

Unique parametrisations for matrices.

Plots of pairwise logratio against a covariable.

Printing compositional data.

Metric summary statistics of real, amount or compositional data

Parallel scalar products

plot in 3D based on rgl

Creates a paneled plot like pairs for two different datasets.

Compute distributions of empirical Mahalanobis distances based on simulations

Loadings of relations of two amounts

Compute the global projector to the observed subspace.

Variogram functions

Residual variance of a model

Axis for ternary diagrams

Simple treatment of real vectors

Compositional variogram model fitting

The jura dataset

acompscalarproduct

inner product for datasets with a vector space structure

kingTetrahedron

Ploting composition into rotable tetrahedron

inner product for matrices and vectors

Total sum of amounts

Modify parameters of compositional plots.

The multivariate lognormal distribution

outliersInCompositions

Analysing outliers in compositions.

Plot various graphics to analyse outliers.

Compositions as elements of the simplex embedded in the D-dimensional real space

Arithmetic operations for compositions in a real geometry

Normalizing datasets by centering and scaling

Draws straight lines.

Summarizing a compositional dataset in terms of ratios

Normal distributions on special spaces

Zero-replacement routine

vectorial arithmetic for data sets with rplus class

Uncentered log transform

Amounts i.e. positive numbers analysed as objects of the real vector space

Empirical variograms for compositions

Splitting datasets in groups given by factors

Variation matrices of amounts and compositions

Variances and covariances of amounts and compositions

simulatemissings

Artifical simulation of various kinds of missings/polluted data

robustnessInCompositions

Handling robustness issues and outliers in compositions.